## [1] "data/config.vertebrata_minimal.yaml"
Analysis report - 20 January, 2023 - 13:08 UTC - version: 0.9.7
Location of genomes files:
results/assemblies
Total number of included genomes: 0
Locally provided genomes: 0
Successfully downloaded genomes: 0
Failed species downloads: 0
Not downloaded:
Information on successfully downloaded genomes:
info <- ""
if (file.exists(downloaded_genomes_statistics_file))
{
if (file.size(downloaded_genomes_statistics_file) != 0) {
data <- read.csv(downloaded_genomes_statistics_file, sep="\t", header=T)
} else {
info <- "*No information about downloaded genomes found. Maybe you only have local species?*"
}
data %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px") # %>% mutate(ftp_path = cell_spec("download", "html", link = ftp_path)) %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px")
} else {
info <- "*No information about downloaded genomes found. Did you run phylociraptor setup ?*"
}
No information about downloaded genomes found. Did you run phylociraptor setup ?
Orthologous genes were inferred using BUSCO.
Location of BUSCO results:
results/orthology/busco
Used BUSCO set: vertebrata_odb10
Total number of BUSCO genes in BUSCO set: 20
Number of BUSCO genes recovered in too few (20) samples: 3
BUSCO genes below threshold:
320238at7742, 164538at7742, 228730at7742
Number of samples with single-copy BUSCO score below threshold (0.5): 0
Genomes below threshold:
| species | single_copy | duplicated | fragmented | missing |
|---|---|---|---|---|
| Amblyraja_radiata | 2999 | 71 | 98 | 186 |
| Anolis_carolinensis | 2861 | 22 | 169 | 302 |
| Callorhinchus_milii | 2976 | 34 | 131 | 213 |
| Canis_lupus | 3122 | 47 | 65 | 120 |
| Danio_kyathit | 3107 | 45 | 75 | 127 |
| Dasypus_novemcinctus | 2717 | 61 | 212 | 364 |
| Eptatretus_burgeri | 1612 | 59 | 490 | 1193 |
| Gallus_gallus | 3180 | 29 | 45 | 100 |
| Homo_sapiens | 2984 | 130 | 77 | 163 |
| Latimeria_chalumnae | 2795 | 30 | 279 | 250 |
| Loxodonta_africana | 3039 | 22 | 103 | 190 |
| Meleagris_gallopavo | 2872 | 19 | 205 | 258 |
| Monodelphis_domestica | 3049 | 142 | 76 | 87 |
| Mus_musculus | 3124 | 55 | 51 | 124 |
| Neoceratodus_forsteri | 2101 | 75 | 723 | 455 |
| Notamacropus_eugenii | 1169 | 29 | 514 | 1642 |
| Oreochromis_niloticus | 3275 | 20 | 25 | 34 |
| Ornithorhynchus_anatinus | 3075 | 36 | 141 | 102 |
| Petromyzon_marinus | 2275 | 59 | 193 | 827 |
| Protopterus_annectens | 2029 | 1130 | 105 | 90 |
| Rana_temporaria | 3088 | 74 | 76 | 116 |
| Scyliorhinus_canicula | 2977 | 102 | 106 | 169 |
| Taeniopygia_guttata | 3161 | 19 | 50 | 124 |
| Takifugu_rubripes | 3120 | 77 | 73 | 84 |
| Xenopus_tropicalis | 3231 | 34 | 30 | 59 |
Location of alignment files:
results/alignments/full
| length | nseqs | nparsimony | nvariable | nfixed | |
|---|---|---|---|---|---|
| 193525at7742_aligned.fas | 652 | 25 | 179 | 617 | 35 |
| 359032at7742_aligned.fas | 347 | 25 | 104 | 325 | 22 |
| 406935at7742_aligned.fas | 291 | 25 | 75 | 275 | 16 |
| 97645at7742_aligned.fas | 1237 | 24 | 290 | 1162 | 75 |
| 332227at7742_aligned.fas | 554 | 23 | 169 | 508 | 46 |
| 361842at7742_aligned.fas | 352 | 25 | 74 | 334 | 18 |
| 409625at7742_aligned.fas | 244 | 25 | 69 | 234 | 10 |
| 33940at7742_aligned.fas | 1351 | 25 | 104 | 1085 | 266 |
| 378120at7742_aligned.fas | 291 | 25 | 108 | 241 | 50 |
| 409719at7742_aligned.fas | 367 | 25 | 73 | 345 | 22 |
| 342641at7742_aligned.fas | 364 | 25 | 128 | 324 | 40 |
| 403632at7742_aligned.fas | 423 | 25 | 34 | 412 | 11 |
| 413149at7742_aligned.fas | 232 | 25 | 75 | 226 | 6 |
| 353318at7742_aligned.fas | 382 | 25 | 89 | 369 | 13 |
| 404316at7742_aligned.fas | 262 | 25 | 66 | 221 | 41 |
| 42971at7742_aligned.fas | 1333 | 23 | 453 | 1043 | 290 |
Location of trimmed alignment files:
results/alignments/trimmed
Parsimony informative sites cutoff: 50
| alignment | length | nseqs | nparsimony | nvariable | nfixed |
|---|---|---|---|---|---|
| 193525at7742_aligned_trimmed.fas | 454 | 25 | 179 | 419 | 35 |
| 359032at7742_aligned_trimmed.fas | 254 | 25 | 104 | 232 | 22 |
| 406935at7742_aligned_trimmed.fas | 197 | 25 | 75 | 181 | 16 |
| 97645at7742_aligned_trimmed.fas | 747 | 24 | 290 | 672 | 75 |
| 332227at7742_aligned_trimmed.fas | 298 | 23 | 169 | 252 | 46 |
| 361842at7742_aligned_trimmed.fas | 217 | 25 | 74 | 199 | 18 |
| 409625at7742_aligned_trimmed.fas | 137 | 25 | 69 | 127 | 10 |
| 33940at7742_aligned_trimmed.fas | 1018 | 25 | 104 | 752 | 266 |
| 378120at7742_aligned_trimmed.fas | 253 | 25 | 108 | 203 | 50 |
| 409719at7742_aligned_trimmed.fas | 135 | 25 | 73 | 113 | 22 |
| 342641at7742_aligned_trimmed.fas | 260 | 25 | 128 | 220 | 40 |
| 403632at7742_aligned_trimmed.fas | 166 | 25 | 34 | 155 | 11 |
| 413149at7742_aligned_trimmed.fas | 124 | 25 | 75 | 118 | 6 |
| 353318at7742_aligned_trimmed.fas | 214 | 25 | 89 | 201 | 13 |
| 404316at7742_aligned_trimmed.fas | 212 | 25 | 66 | 171 | 41 |
| 42971at7742_aligned_trimmed.fas | 1026 | 23 | 453 | 736 | 290 |
Location of filtered alignment files:
results/alignments/filtered
Parsimony informative sites cutoff: 50
| alignment | length | nseqs | nparsimony | nvariable | nfixed |
|---|---|---|---|---|---|
| 193525at7742_aligned_trimmed.fas | 454 | 25 | 179 | 419 | 35 |
| 359032at7742_aligned_trimmed.fas | 254 | 25 | 104 | 232 | 22 |
| 409625at7742_aligned_trimmed.fas | 137 | 25 | 69 | 127 | 10 |
| 332227at7742_aligned_trimmed.fas | 298 | 23 | 169 | 252 | 46 |
| 361842at7742_aligned_trimmed.fas | 217 | 25 | 74 | 199 | 18 |
| 409719at7742_aligned_trimmed.fas | 135 | 25 | 73 | 113 | 22 |
| 33940at7742_aligned_trimmed.fas | 1018 | 25 | 104 | 752 | 266 |
| 378120at7742_aligned_trimmed.fas | 253 | 25 | 108 | 203 | 50 |
| 413149at7742_aligned_trimmed.fas | 124 | 25 | 75 | 118 | 6 |
| 342641at7742_aligned_trimmed.fas | 260 | 25 | 128 | 220 | 40 |
| 404316at7742_aligned_trimmed.fas | 212 | 25 | 66 | 171 | 41 |
| 42971at7742_aligned_trimmed.fas | 1026 | 23 | 453 | 736 | 290 |
| 353318at7742_aligned_trimmed.fas | 214 | 25 | 89 | 201 | 13 |
| 406935at7742_aligned_trimmed.fas | 197 | 25 | 75 | 181 | 16 |
| 97645at7742_aligned_trimmed.fas | 747 | 24 | 290 | 672 | 75 |
Location of modeltesting files:
results/modeltest
Overview of individual modeltest results: | alignment | clustalo-trimal |
|---|---|
| 404316at7742 | JTT+R3 |
| 406935at7742 | VT+G4 |
| 97645at7742 | JTT+R3 |
| 361842at7742 | JTTDCMut+G4 |
| 413149at7742 | JTTDCMut+G4 |
| 409719at7742 | LG+G4 |
| 332227at7742 | JTT+G4 |
| 42971at7742 | JTT+I+G4 |
| 409625at7742 | JTT+I+G4 |
| 193525at7742 | JTT+G4 |
| 353318at7742 | JTT+G4 |
| 378120at7742 | JTTDCMut+F+R3 |
| 342641at7742 | LG+I+G4 |
| 359032at7742 | JTT+I+G4 |
| 33940at7742 | VT+R2 |
Location of gene trees:
results/modeltest
| gene | clustalo-trimal |
|---|---|
| 404316at7742 | 81 |
| 406935at7742 | 75 |
| 97645at7742 | 83 |
| 361842at7742 | 79 |
| 413149at7742 | 77 |
| 409719at7742 | 66 |
| 332227at7742 | 87 |
| 42971at7742 | 87 |
| 409625at7742 | 76 |
| 193525at7742 | 87 |
| 353318at7742 | 83 |
| 378120at7742 | 75 |
| 342641at7742 | 75 |
| 359032at7742 | 78 |
| 33940at7742 | 83 |
Location of phylogenetic results:
results/phylogeny-*/
| software | aligner | trimmer | boostraps | bootstrap-cutoff | ngenes | tree |
|---|---|---|---|---|---|---|
| iqtree | clustalo | trimal | 1000 | 80 | 7 |
Location of phylogenetic results:
results/phylogeny-*/
| software | aligner | trimmer | bootstrap-cutoff | ngenes | tree |
|---|---|---|---|---|---|
| astral | clustalo | trimal | 80 | 7 |
## Fri Jan 20 12:37:08 UTC 2023 - Pipeline part 1 (orthology) done.
## Fri Jan 20 12:37:30 UTC 2023 - BUSCO files will be filtered on a per-sample basis. This could lower the number of species in the final tree.
## Fri Jan 20 12:37:32 UTC 2023 - Number of BUSCO sequence files: 16
## Fri Jan 20 12:37:32 UTC 2023 - Number of deduplicated BUSCO sequence files: 16
## Fri Jan 20 12:37:32 UTC 2023 - Pipeline part filter-orthology done.
## Fri Jan 20 12:39:48 UTC 2023 - Pipeline part 2 (align) done.
## Fri Jan 20 12:40:42 UTC 2023 - Number of alignments (clustalo): 16
## Fri Jan 20 12:40:42 UTC 2023 - Number of trimmed alignments (clustalo - trimal): 16
## Fri Jan 20 12:40:42 UTC 2023 - Number of alignments (clustalo - trimal) after filtering: 15
## Fri Jan 20 12:40:46 UTC 2023 - Pipeline part filter_align done.
## Fri Jan 20 12:47:06 UTC 2023 - Pipeline part modeltest (model) done.
## Fri Jan 20 12:48:13 UTC 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Fri Jan 20 12:48:14 UTC 2023 - Speciestree reconstruction done.
## Fri Jan 20 13:03:05 UTC 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Fri Jan 20 13:03:05 UTC 2023 - nexus file for iqtree written.
## Fri Jan 20 13:04:56 UTC 2023 - Pipeline part 3 (tree) done.